Application Note Number 103: Use of Trend Mode XML Data in Excel
Abstract: XML data from the VacuumPlus software has a fixed format as shown
in the Extorr manual. This same format is used to encapsulate the output from the
Trend mode as well. This application note discusses how to use this XML data
output in Microsoft Excel to parse, adjust and display this data. An example of
breathing into a vacuum chamber by means of a restrictive capillary is given.
In response to a request, an Extorr system was set up in the Trend Mode to monitor five peaks within
100 ms. In the Trend mode the software reports the maximum value of five equally spaced mass
positions within a quarter of an amu of the exact mass position. This corrects for any possible mass
errors in tunings or mass defects. The dwell times given must each be multiplied by five to arrive at
the time spent at each nominal mass position. We chose to monitor peaks 26, 28, 32, 44, and 4. The
single dwell times added up to 20.5 ms for a total dwell time of about 100 ms. This set up is shown
in the screen shot below.
A fused silica capillary was used as an inlet to a turbopumped vacuum system which contains an
Extorr RGA. The end of the capillary was placed into a quarter inch plastic tube into which we
breathed in and out. This was displayed on the Vacuum Plus GUI as was shown above.
The data shown on the graph is available for further analysis by exporting it using the File>Save as
XML sequence. The accumulated data is placed in an XML formatted file which may be read in a
browser.
This data may then also be imported into any other program which supports the XML format. In
particular, the file may be imported into Microsoft Excel using Data>Import External Data>Import
Data. Just insert the name and location of your file in the resulting file dialog box and the data is
entered into Excel in the form below.
Note that this is the same data format as the sweep data. The only part of the data which is useful is
the information in column J. Also note that the data is given in groups of five, one data point for each
of the masses in one time interval. It is now not that easy to do further analysis on this data manually
but Excel macros may be written in VBA to deconvolute the data. The macro below asks for
information about the data set, the name of the file on the desktop and then sorts each mass output in
its own column.
Sub Deconvolute()
'
' Deconvolute() will ask for .xml files located in the C: directory.
' Information about the data set is asked for and the single data
' column will deconvolute into single mass columns .
'
ActiveCell.FormulaR1C1 = "# Samples" 'Fill out new column labels.
Range("C1").Select
ActiveCell.FormulaR1C1 = "Mass1"
Range("D1").Select
ActiveCell.FormulaR1C1 = "Mass2"
Range("E1").Select
ActiveCell.FormulaR1C1 = "Mass3"
Range("F1").Select
ActiveCell.FormulaR1C1 = "Mass4"
Range("G1").Select
ActiveCell.FormulaR1C1 = "Mass5"
Range("H1").Select
ActiveCell.FormulaR1C1 = "Mass6"
Range("I1").Select
ActiveCell.FormulaR1C1 = "Mass7"
Range("J1").Select
ActiveCell.FormulaR1C1 = "Mass8"
Range("K1").Select
ActiveCell.FormulaR1C1 = "Mass9"
Range("L1").Select
ActiveCell.FormulaR1C1 = "Mass10"
Range("B1").Select
ActiveCell.FormulaR1C1 = "# Masses"
Range("A2").Select
ActiveCell.FormulaR1C1 = InputBox("Enter the number of sampes taken")
Range("B2").Select
ActiveCell.FormulaR1C1 = InputBox("Enter the number of masses measured")
Range("C2").Select
' Input masses used
For x = 1 To Range("B2")
ActiveCell.FormulaR1C1 = InputBox("Enter Mass")
ActiveCell.Offset(0, 1).Select
Next
' Input .xml file starting at "A3".
Range("A3").Select
Filename$ = InputBox("Enter name of file located in C: on desktop(do not type .xml extension)")
With ActiveSheet.QueryTables.Add(Connection:= _
"FINDER;C:\" + Filename$ + ".xml", _
Destination:=Range("A3"))
.Name = "Breath"
.FieldNames = True
.RowNumbers = False
.FillAdjacentFormulas = False
.PreserveFormatting = True
.RefreshOnFileOpen = False
.BackgroundQuery = True
.RefreshStyle = xlInsertDeleteCells
.SavePassword = False
.SaveData = True
.AdjustColumnWidth = True
.RefreshPeriod = 0
.WebSelectionType = xlAllTables
.WebFormatting = xlWebFormattingNone
.WebPreFormattedTextToColumns = True
.WebConsecutiveDelimitersAsOne = True
.WebSingleBlockTextImport = False
.WebDisableDateRecognition = False
.WebDisableRedirections = False
.Refresh BackgroundQuery:=False
End With
'Clean out unused headers.
Range("A3:P4").Select
Selection.Delete Shift:=xlUp
Range("A3:I1503").Select
Selection.Delete Shift:=xlToLeft
'Do the deconvolution.
For x = 0 To Range("A2")
For z = 1 To Range("B2")
y$ = Chr(66 + z) + Trim(Str$(x + 4))
Range("A3").Select
Selection.Cut
Range(y$).Select
ActiveSheet.Paste
Range("A3").Select
Selection.Delete Shift:=xlUp
Selection.Cut
Next z
Next x
End Sub
As we do this, we can also do further analysis. For instance, the data was taken in terms of partial
pressures in torr. If we would like the results in terms of percentage, a first order result would be
given by multiplying each value by 100 and dividing by the sum of all readings in each time interval.
This could be further refined by multiplying each mass output by a sensitivity value which takes into
account the relative cross section for ionization and the cracking pattern for each of the gases being
monitored. We also need to establish a time base by placing the time taken for each sample. The
macro below does this for the data above.
Sub Analyze5()
' Uses relative sensitivity factors of 1.07 for Oxygen and
' 0.8 for Carbon dioxide, normalizes data to 100% and places
' new data in columns I through G
For x = 1 To Range("A2")
Range("I" + Trim(Str$(x + 3))).Select
ActiveCell.FormulaR1C1 = _
"=RC[-6]*100/(RC[-6]+RC[-5]+1.07*RC[-4]+0.8*RC[-3]+RC[-2])"
Range("J" + Trim(Str$(x + 3))).Select
ActiveCell.FormulaR1C1 = _
"=RC[-6]*100/(RC[-7]+RC[-6]+1.07*RC[-5]+0.8*RC[-4]+RC[-3])"
Range("K" + Trim(Str$(x + 3))).Select
ActiveCell.FormulaR1C1 = _
"=RC[-6]*107/(RC[-8]+RC[-7]+1.07*RC[-6]+0.8*RC[-5]+RC[-4])"
Range("L" + Trim(Str$(x + 3))).Select
ActiveCell.FormulaR1C1 = _
"=RC[-6]*80/(RC[-9]+RC[-8]+1.07*RC[-7]+0.8*RC[-6]+RC[-5])"
Range("M" + Trim(Str$(x + 3))).Select
ActiveCell.FormulaR1C1 = _
"=RC[-6]*100/(RC[-10]+RC[-9]+1.07*RC[-8]+0.8*RC[-7]+RC[-6])"
Next
End Sub and displays the data on a plot as a function of time.
Time data may then be applied by the MakeTime macro below.
Sub MakeTime()
'
' MakeTime Macro
' This asks for the time information and makes time
'
Range("H4").Select
TimeInt = InputBox("Enter the sum of the dwell times for the sampes taken.")
For x = 1 To Range("A2")
ActiveCell.Value = 5 * x * TimeInt
ActiveCell.Offset(1, 0).Select
Next x
End Sub
Finally this data may be plotted using the plot macro below.
Sub MakeTrendPlot5()
'
' MakeTrendPlot5 Macro
'
Range("H4:M303").Select
Range("M303").Activate
Charts.Add
ActiveChart.ChartType = xlXYScatterSmoothNoMarkers
ActiveChart.SetSourceData Source:=Sheets("Sheet1").Range("H4:M303"), PlotBy _
:=xlColumns
ActiveChart.SeriesCollection(1).Name = "=""26"""
ActiveChart.SeriesCollection(2).Name = "=""28"""
ActiveChart.SeriesCollection(3).Name = "=""32"""
ActiveChart.SeriesCollection(4).Name = "=""44"""
ActiveChart.SeriesCollection(5).Name = "=""4"""
ActiveChart.Location Where:=xlLocationAsObject, Name:="Sheet1"
With ActiveChart
.HasTitle = True
.ChartTitle.Characters.Text = "Breathing"
.Axes(xlCategory, xlPrimary).HasTitle = True
.Axes(xlCategory, xlPrimary).AxisTitle.Characters.Text = "Time (seconds)"
.Axes(xlValue, xlPrimary).HasTitle = True
.Axes(xlValue, xlPrimary).AxisTitle.Characters.Text = "Molecular Percent"
End With
Windows("SortTrend .xls").ScrollRow = 3
Windows("SortTrend .xls").ScrollRow = 2
Windows("SortTrend .xls").ScrollRow = 1
ActiveSheet.Shapes("Chart 1").IncrementLeft -284.25
ActiveSheet.Shapes("Chart 1").IncrementTop -192#
ActiveWindow.Visible = False
Windows("SortTrend .xls").Activate
Range("Q31").Select
End Sub
The net result of all of these macros is the Excel Page below.
This, of course, is not the complete picture of breath analysis since, for instance, we did not deal with
water vapor which is also vastly different for the inhaled and exhaled air. This note is only intended
to show how Excel macros may be used to refine and display raw data.